The current study was carried out on three Egyptian dairy herds located at Alexandria, Ismailia and Mansoura, from 2009 to 2012. Those herds were suffering from clinical or subclinical infection of Mycobacterium avium subspecies paratuberculosis (MAP). The objective from this work is to identify circulating strains in some Egyptian dairy herds. Animals were tested for detection of anti Mycobacterium paratuberculosis antibodies by ELISA test. Animal fecal samples were cultured on Herrold's egg yolk medium (HEYM) supplemented with mycobactin-J. The confirmed positive results used for isolation of “MAP" from 11 out of 23 samples. Moreover, results of real time- PCR specific for IS900 gene of M. paratuberculosis on 23 fecal samples indicated the positivity of 21 fecal samples. Five bacterial isolates (two from Alexandria, two from Ismailia and one from Mansoura) were subjected to conventional PCR targeting a 413-bp fragment of the IS900. The 413 bp PCR purified product were subjected to sequencing. The obtained sequences were aligned and compared to other international strains of MAP using Basic Local Aligment Search Tool (BLAST). The sequencing data shows that 3 isolates were identical to each other (100%) and to other strains from Europe (UK, Spain, Netherlands, Slovakia, Germany and Italy); the other 2 isolates show 98% similarity. Authors recommended that establishment of strict measures for mycobacterium avium subspecies paratuberculosis infections by the Egyptian authorities is very important.